SMTL ID : 7cy8.1

Crystal Structure of CMD1 in complex with 5mC-DNA and vitamin C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ASC: ASCORBIC ACID(Non-covalent)

ASC.1: 14 residues within 4Å: Chain A: V.625, S.709, T.711, V.716, H.719, I.730, F.745, H.771, G.772, T.773, G.786, S.788 Chain C: C.3 Ligands: FE2.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.709, A:S.709, A:T.711, A:T.773, A:S.788 Water bridges: A:R.618, A:T.711, A:Q.714, A:W.732, A:S.788

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: E.112, Y.156 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: R.514, F.619, M.717, H.719, L.720 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.720, A:L.720

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 2 residues within 4Å: Chain A: D.605, S.609 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.609

1 x FE2: FE (II) ION(Non-covalent)

FE2.5: 5 residues within 4Å: Chain A: R.618, H.719, D.721, H.771 Ligands: ASC.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.719, A:D.721, A:H.771, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1. Nat Commun (2021)

Release Date

2020-12-30

Peptides

Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1

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